ID:

dvi_8721

 Coordinate:

scaffold_12928:3299151-3299301 -

 Confidence:

Candidate

 Type:

Unknown

 [View on UCSC Genome Browser {Cornell Mirror}]
Legend: mature star mismatch in alignment mismatch in read

Predicted structure

-33.8 -33.7 -33.7

Flybase annnotation

exon [dvir_GLEANR_17082:4]; CDS [Dvir\GJ16574-cds]; intron [Dvir\GJ16574-in]

No Repeatable elements found

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
TCAAGCAGAGGCTTTGTGGATATGATATTTGATAGCGTGGTGTCCCATCGGGTAGCTCGTCTTCCTTAGCTTGTAGGAGGCTCGAATAGCAGCGTTTATTAGAATCAATTAGAGGGGAACCCGACTGGACTCTTGCCAGCTTGTCCGTTGCTTCCAATCTTTCTTATTTTCGCTTAACGTGTTTTCGGTTTCTTTGGACAGGTCTACAGTCCGTTTCAGTTCTGGTTTCATGTTGTTGGCGGCGACTATGA
**************************************************...((((..........))))...(((((((.((((.((((.((((.....(((......(((..((((..((((.((((............)))))))).))))..)))........)))....))))))))))))))))))).......************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060681
Argx9_testes_total
 SRR060678
9x140_testes_total
 SRR060655
9x160_testes_total
 SRR060659
Argentina_testes_total
 SRR060680
 9xArg_testes_total
 SRR060682
9x140_0-2h_embryos_total
 SRR060684
140x9_0-2h_embryos_total
 SRR060686
Argx9_0-2h_embryos_total
 SRR060689
160x9_testes_total
 V053
head
 M047
female body
 SRR1106729
mixed whole adult body
 M027
male body		 SRR060679
140x9_testes_total
 V047
embryo
........................ATATTTGATAGCGTGGTGTCC.............................................................................................................................................................................................................. 21 0 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
........................................TGTCCCATCGGGTAGCTCGTCTTCCTT........................................................................................................................................................................................ 27 0 1 1.00 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
............................................................................................................................................................................................................................TCTGGTTTCATGTTGTTGGC........... 20 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
................................TAGCGTGGTGTCCCATCGGGTAGC................................................................................................................................................................................................... 24 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................................TTTCGGTTTCTTTGGACAGGTC............................................... 22 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................................................................................................................................................GGTTTCATGTTGTTGGCG.......... 18 0 1 1.00 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
.........................................GTCCCATCGGGTAGCTCGTCTTCCTTAGC..................................................................................................................................................................................... 29 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
........................................................................................................................................................................................................................CAGTTCTGGTTTCATGTTGTTGGCGG......... 26 0 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
.............................................................................................................TAGAGGGGAACCCGACTGGACTCTTG.................................................................................................................... 26 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..........................................................................................................................................................................................................................GTTCTGGTTTCATGTTGTTGGCGGC........ 25 0 1 1.00 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
........................................TGTCCCTTCGGTTAGCTGGTC.............................................................................................................................................................................................. 21 3 2 0.50 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
........................................TGACCCATCGGTTAGCTTGT............................................................................................................................................................................................... 20 3 3 0.33 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
..................................................................................................................................................................................................................CCGTCTCAGTTCGGGTTGCA..................... 20 3 3 0.33 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
................................................................................................................AGAGGAACACTACTGGACT........................................................................................................................ 19 3 6 0.17 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
............................................................................................................................................TTCTTCGCTGCTTCCAATCT........................................................................................... 20 3 19 0.05 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
.........................TAGTTGACAGTGTGGTGTC............................................................................................................................................................................................................... 19 3 20 0.05 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................................................AGGGGAACCTGACTGTCC......................................................................................................................... 18 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
......................................................GCTCGGCTTCCTCAGCCTG.................................................................................................................................................................................. 19 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
.............................................................................................................TGGTGGGGAATCCGACTG............................................................................................................................ 18 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0

Anti-sense strand reads

AGTTCGTCTCCGAAACACCTATACTATAAACTATCGCACCACAGGGTAGCCCATCGAGCAGAAGGAATCGAACATCCTCCGAGCTTATCGTCGCAAATAATCTTAGTTAATCTCCCCTTGGGCTGACCTGAGAACGGTCGAACAGGCAACGAAGGTTAGAAAGAATAAAAGCGAATTGCACAAAAGCCAAAGAAACCTGTCCAGATGTCAGGCAAAGTCAAGACCAAAGTACAACAACCGCCGCTGATACT
**************************************************...((((..........))))...(((((((.((((.((((.((((.....(((......(((..((((..((((.((((............)))))))).))))..)))........)))....))))))))))))))))))).......************************************************** 		Read size # Mismatch Hit Count Total Norm Total V116
male body		 SRR060680
 9xArg_testes_total
 SRR060688
160_ovaries_total
 V047
embryo
 M047
female body
 GSM1528803
follicle cells		 SRR060672
9x160_females_carcasses_total
 M027
male body		 SRR060682
9x140_0-2h_embryos_total
 SRR060662
9x160_0-2h_embryos_total
 SRR060673
9_ovaries_total
 V053
head
 SRR060658
140_ovaries_total
 SRR060669
160x9_females_carcasses_total
 SRR060679
140x9_testes_total
 SRR060687
9_0-2h_embryos_total
 SRR1106714
embryo_2-4h
 SRR060665
9_females_carcasses_total
 SRR060666
160_males_carcasses_total
 SRR060667
160_females_carcasses_total
 M061
embryo
 SRR060661
160x9_0-2h_embryos_total
 SRR060671
9x160_males_carcasses_total
 SRR060654
160x9_ovaries_total
.....................................................................GGACATCCCCCGAGCTTG.................................................................................................................................................................... 18 3 18 3.11 56 18 0 0 0 15 0 9 0 2 3 0 0 0 2 2 2 0 0 0 0 1 1 1 0
...............................................................................................................................................................................................................TCAGGCAAAGTCAAGACCAAA....................... 21 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................................................................................................................................................CAGGAAAAGTCAAGACGAAAGT..................... 22 2 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................................................................CTTGGGCTGACCTGAGAACGG.................................................................................................................. 21 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
........................................................................CATCCTCTGAGCTTATGCTC............................................................................................................................................................... 20 3 4 0.50 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................GGGACATCCCCCGAGCTT..................................................................................................................................................................... 18 3 16 0.31 5 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 1 1 0 0 0 0
...............................................................................................................................................................................................................TCAGGCAAGGTCAAGAC........................... 17 1 5 0.20 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................................................................................................................................................................GGAAAGTCCAGGCCAAAGTA.................... 20 3 5 0.20 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
............................AACTATCGAACGATAGGGTA........................................................................................................................................................................................................... 20 3 7 0.14 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
.....................................................................................................................................................................................................TGTCAAGATGTCAGTCAAA................................... 19 2 7 0.14 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................................................................................................................................................CAGGCGAAGTCAAGACTCAA....................... 20 3 12 0.08 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
..........................................................................................................................................................................TCGAATTGCACAAAAGAAAAAG........................................................... 22 3 16 0.06 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.....................................................................GCACATCCCCCGAGCTTG.................................................................................................................................................................... 18 3 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..........................................AGGGTAGCCGGTGGAGCAG.............................................................................................................................................................................................. 19 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droVir3 scaffold_12928:3299101-3299351 - dvi_8721 TCAAGCAGAGGCTTTGTGGATATGATATTTGATAGCGTGGTGTCCCATCGGGTAGCTCGTCTTCCTTAGCTTGTAGGAGGCTCGAATAGCAGCGTTTATTAGAATCAATTAGAGGGGAACCCGACTGGACTCTTGCCAGCTTGTCCGTTGCTTCCAATCTTTCTTATTTTCGCTTAACGTGTTTTCGGTTTCTTTGGACAGGTCTACAGTCCGTTTCAGTTCTGGTTTCATGTTGTTGGC-----GGCGACTATGA
droMoj3 scaffold_6308:169836-169888 - ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGCCTACAGCCCCTTTCAGTTCTGGTTCCATATTGCTGAG-----GGCCCCTACGA
dp5 XL_group1a:3918856-3918908 + ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGTGTACAGCCCCTTTCAGTTTTGGTTCCAAATCGCTGAG-----GAAAATTATGC
droPer2 scaffold_11:481820-481871 + ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGTGTACAGCCCCTTTCAGTTTTGGTTCCAAATCGCTGAG-----GAAAATTATG-
droFic1 scf7180000454045:326211-326262 - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTTTATAGTCCGTTTCAGTTTTGGTTTCATTTTGTGGGC-----ACAATGTACGA
droEle1 scf7180000491272:221646-221703 + TC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCATAGGTTTACAGTCCATTTCAGTTTTGGTTTCATTTCGTAAAC-----GGCTTCCAAGA
droRho1 scf7180000779588:250670-250721 - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTTTATAGTCCTTTTCAGTTTTGGTTCCATTTTGTAAAT-----AGCTCGCACGA
droBia1 scf7180000301345:295642-295679 + ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGTCTATAGCCCCTTTCAGTTCTGGTTCCATTTCGT--------------------
droTak1 scf7180000415769:427107-427147 - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTCTACAGTCCCTTTCAGTTTTGGTTCCAATTCGTGGAC----------------
droYak3 X:3255390-3255441 + -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTGTACAGTCCCTTTCAGTTCTGGTTCCACTTTCAGCAT-----CCCACGGACGA
droEre2 scaffold_4690:2565851-2565907 - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTACAGTCCTTTTCAGTTCTGGTTTCACTTTGTGCCACCGGTTGATGGCGACG

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droVir3
TCAAGCAGAGGCTTTGTGGATATGATATTTGATAGCGTGGTGTCCCATCGGGTAGCTCGTCTTCCTTAGCTTGTAGGAGGCTCGAATAGCAGCGTTTATTAGAATCAATTAGAGGGGAACCCGACTGGACTCTTGCCAGCTTGTCCGTTGCTTCCAATCTTTCTTATTTTCGCTTAACGTGTTTTCGGTTTCTTTGGACAGGTCTACAGTCCGTTTCAGTTCTGGTTTCATGTTGTTGGC-----GGCGACTATGASizeHit CountTotal NormTotalM027
Male-body		M028
Head		M047
Female-body		M061
Embryo		SRR060654
Ovary		SRR060655
Testis		SRR060656
Ovary		SRR060657
Testis		SRR060658
Ovary		SRR060659
Testis		SRR060660
Ovary		SRR060661
Embryo		SRR060662
Embryo		SRR060663
Embryo		SRR060664
Male-body		SRR060665
Female-body		SRR060666
Male-body		SRR060667
Female-body		SRR060668
Male-body		SRR060669
Female-body		SRR060670
Testis		SRR060671
Male-body		SRR060672
Female-body		SRR060673
Ovary		SRR060674
Ovary		SRR060675
Ovary		SRR060676
Ovary		SRR060677
Ovary		SRR060678
Testis		SRR060679
Testis		SRR060680
Testis		SRR060681
Testis		SRR060682
Embryo		SRR060683
Testis		SRR060684
Embryo		SRR060685
Embryo		SRR060686
Embryo		SRR060687
Embryo		SRR060688
Ovary		SRR060689
Testis		SRR1106712
embryo_0-2h		SRR1106713
embryo_0-2h		SRR1106714
embryo_2-4h		SRR1106715
embryo_4-6h		SRR1106716
embryo_4-6h		SRR1106717
embryo_6-8h		SRR1106718
embryo_6-8h		SRR1106719
embryo_8-10h		SRR1106720
embryo_8-10h		SRR1106721
embryo_10-12h		SRR1106722
embryo_10-12h		SRR1106723
embryo_12-14h		SRR1106724
embryo_12-14h		SRR1106725
embryo_14-16h		SRR1106726
embryo_14-16h		SRR1106727
larvae		SRR1106728
larvae		SRR1106729
mixed whole adult body		SRR1106730
embryo_16-30h		V047
Embryo		V053
Head		V116
Male-body		GSM1528803
follicle cells
........................ATATTTGATAGCGTGGTGTCC...................................................................................................................................................................................................................2111.001000000000100000000000000000000000000000000000000000000000000000
........................................TGTCCCATCGGGTAGCTCGTCTTCCTT.............................................................................................................................................................................................2711.001000000000000000000000000000000000000000100000000000000000000000
............................................................................................................................................................................................................................TCTGGTTTCATGTTGTTGGC-----...........2011.001000000000000000000000000000010000000000000000000000000000000000
................................TAGCGTGGTGTCCCATCGGGTAGC........................................................................................................................................................................................................2411.001000000000000000000000000000000010000000000000000000000000000000
......................................................................................................................................................................................TTTCGGTTTCTTTGGACAGGTC....................................................2211.001000001000000000000000000000000000000000000000000000000000000000
...............................................................................................................................................................................................................................GGTTTCATGTTGTTGGC-----G..........1811.001000000000000000000000000000000000010000000000000000000000000000
.........................................GTCCCATCGGGTAGCTCGTCTTCCTTAGC..........................................................................................................................................................................................2911.001000000000000000000000000000000100000000000000000000000000000000
........................................................................................................................................................................................................................CAGTTCTGGTTTCATGTTGTTGGC-----GG.........2611.001000000000000000000000000000000000000100000000000000000000000000
.............................................................................................................TAGAGGGGAACCCGACTGGACTCTTG.........................................................................................................................2611.001000000000000000000000000000000010000000000000000000000000000000
..........................................................................................................................................................................................................................GTTCTGGTTTCATGTTGTTGGC-----GGC........2511.001000000000000000000000000000000001000000000000000000000000000000
droMoj3
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGCCTACAGCCCCTTTCAGTTCTGGTTCCATATTGCTGAG-----GGCCCCTACGASizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
No Reads
dp5
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGTGTACAGCCCCTTTCAGTTTTGGTTCCAAATCGCTGAG-----GAAAATTATGCSizeHit CountTotal NormTotalM022
Male-body		M040
Female-body		M059
Embryo		M062
Head		V043
Embryo		V051
Head		V112
Male-body		SRR902010
Ovary		SRR902011
Testis		SRR902012
CNS imaginal disc
No Reads
droPer2
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGTGTACAGCCCCTTTCAGTTTTGGTTCCAAATCGCTGAG-----GAAAATTATG-SizeHit CountTotal NormTotalM021
Embryo		M042
Female-body		V042
Embryo		V050
Head		V057
Head		V111
Male-body
No Reads
droFic1
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTTTATAGTCCGTTTCAGTTTTGGTTTCATTTTGTGGGC-----ACAATGTACGASizeHit CountTotal NormTotal
No Reads
droEle1
TC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCATAGGTTTACAGTCCATTTCAGTTTTGGTTTCATTTCGTAAAC-----GGCTTCCAAGASizeHit CountTotal NormTotal
No Reads
droRho1
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTTTATAGTCCTTTTCAGTTTTGGTTCCATTTTGTAAAT-----AGCTCGCACGASizeHit CountTotal NormTotal
No Reads
droBia1
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGTCTATAGCCCCTTTCAGTTCTGGTTCCATTTCGT--------------------SizeHit CountTotal NormTotal
No Reads
droTak1
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTCTACAGTCCCTTTCAGTTTTGGTTCCAATTCGTGGAC----------------SizeHit CountTotal NormTotal
No Reads
droYak3
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGTGTACAGTCCCTTTCAGTTCTGGTTCCACTTTCAGCAT-----CCCACGGACGASizeHit CountTotal NormTotalM026
Head		M043
Female-body		M056
Embryo		V046
Embryo		V052
Head		V058
Head		V120
Male-body		SRR1275488
Male larvae		SRR1275486
Male prepupae		SRR1275484
Male prepupae		GSM1528802
follicle cells
No Reads
droEre2
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTACAGTCCTTTTCAGTTCTGGTTTCACTTTGTGCCACCGGTTGATGGCGACGSizeHit CountTotal NormTotalM055
Female-body		M057
Embryo		V060
Head		V040
Embryo		V107
Male-body		V108
Head		GSM1528801
follicle cells
No Reads

Generated: 05/16/2015 at 10:02 PM